title: Cotranscriptional recruitment of yeast TRAMP complex to intronic sequences promotes optimal pre-mRNA splicing.
abstract: Most unwanted RNA transcripts in the nucleus of eukaryotic cells, such as splicing-defective pre-mRNAs and spliced-out introns, are rapidly degraded by the nuclear exosome. In budding yeast, a number of these unwanted RNA transcripts, including spliced-out introns, are first recognized by the nuclear exosome cofactor Trf4/5p-Air1/2p-Mtr4p polyadenylation (TRAMP) complex before subsequent nuclear-exosome-mediated degradation. However, it remains unclear when spliced-out introns are recognized by TRAMP, and whether TRAMP may have any potential roles in pre-mRNA splicing. Here, we demonstrated that TRAMP is cotranscriptionally recruited to nascent RNA transcripts, with particular enrichment at intronic sequences. Deletion of TRAMP components led to further accumulation of unspliced pre-mRNAs even in a yeast strain defective in nuclear exosome activity, suggesting a novel stimulatory role of TRAMP in splicing. We also uncovered new genetic and physical interactions between TRAMP and several splicing factors, and further showed that TRAMP is required for optimal recruitment of the splicing factor Msl5p. Our study provided the first evidence that TRAMP facilitates pre-mRNA splicing, and we interpreted this as a fail-safe mechanism to ensure the cotranscriptional recruitment of TRAMP before or during splicing to prepare for the subsequent targeting of spliced-out introns to rapid degradation by the nuclear exosome.
authors.affiliation: Department of Biochemistry, Department of Medicine, State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong and Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Ka-Yiu Edwin
authors.initials: KY
authors.lastname: Kong
authors.forename: Hei-Man Vincent
authors.initials: HM
authors.lastname: Tang
authors.forename: Kewu
authors.initials: K
authors.lastname: Pan
authors.forename: Zhe
authors.initials: Z
authors.lastname: Huang
authors.forename: Tsz-Hang Jimmy
authors.initials: TH
authors.lastname: Lee
authors.forename: Alan G
authors.initials: AG
authors.lastname: Hinnebusch
authors.forename: Dong-Yan
authors.initials: DY
authors.lastname: Jin
authors.forename: Chi-Ming
authors.initials: CM
authors.lastname: Wong
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D053487:DEAD-box RNA Helicases / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000235:genetics / Q000378:metabolism; D063326:Exosome Multienzyme Ribonuclease Complex / Q000378:metabolism; D017353:Gene Deletion; D017930:Genes, Reporter; D007438:Introns; D012322:RNA Precursors / Q000378:metabolism*; D012326:RNA Splicing; D000072260:RNA Splicing Factors; D012333:RNA, Messenger / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000235:genetics; D012261:Ribonucleoproteins / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D000072668:Splicing Factor U2AF; D061805:Transcription Elongation, Genetic; D014158:Transcription, Genetic; D001616:beta-Galactosidase / Q000235:genetics
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C415824:Air1 protein, S cerevisiae; C415825:Air2 protein, S cerevisiae; C490347:MSL1 protein, S cerevisiae; C409040:MSL5 protein, S cerevisiae; C089980:MUD2 protein, S cerevisiae; D012322:RNA Precursors; D000072260:RNA Splicing Factors; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D016601:RNA-Binding Proteins; D017413:Ribonucleoprotein, U2 Small Nuclear; D012261:Ribonucleoproteins; D029701:Saccharomyces cerevisiae Proteins; D000072668:Splicing Factor U2AF; D004259:DNA-Directed DNA Polymerase; C487545:PAP2 protein, S cerevisiae; D063326:Exosome Multienzyme Ribonuclease Complex; C112610:RRP6 protein, S cerevisiae; D001616:beta-Galactosidase; C101004:MTR4 protein, S cerevisiae; D053487:DEAD-box RNA Helicases